Figure 3: 3D conformations of 14 dsDNA structures.

Conformations obtained by flexibly fitting the dsDNA model onto the EM density maps using targeted MD simulations. (a) The final density map provided a constraint for the TMD simulations to achieve a new DNA conformation. Four snapshot images during the TMD simulation illustrate the process of flexibly docking the DNA model into the IPET density map to achieve a new conformation of DNA (arrow indicated the great conformational changing portion of DNA). During this process, the DNA conformation was allowed to change its structure while maintaining its chemical geometry and bonds with local energy minimization. (b) The final conformation of the second dsDNA structure was obtained from the second density map by following the same processes. (c–e) Gallery of 12 additional conformations from the 3D density maps of an additional 12 DNA-nanogold conjugates reconstructed using IPET. (c) Selected projections of the 3D density map of each individual DNA-nanogold conjugate. (d) Final 3D density maps of the individual DNA-nanogold conjugates. (e) The overlaid density maps of the final 3D reconstruction (grey) and its reversed contrast map (gold) revealed the overall conformation of the DNA-nanogold conjugates. A standard 84-bp dsDNA structure was flexibly docked into each density map to achieve the new conformations via TMD simulations. (f) Conformational flexibility and dynamics of the DNA-nanogold conjugate. Fourteen conformations of the DNA-nanogold conjugates were aligned together based on their first 14 bp. The distribution of dsDNA is shown from three orthogonal views. Scale bars=5 nm (a,b) and 10 nm (c–e).